This notebook will begin looking at clustering methods on the expression of the genes in a single sample of the dataset of interest, from an unbiased approach.
# Load libraries
library(magrittr)
library(scater)
library(readr)
library(bluster)
library(ggpubr)
library(pheatmap)
# Set file paths
data_dir <- file.path("results", "Gawad_processed_data")
# Source custom functions script
source(file.path("utils", "clustering-functions.R"))
sample_290_normalized <- read_rds(
file.path(data_dir, "SCPCS000216", "SCPCL000290_miQC_downstream_processed_normalized_reduced_sce.rds"))
# Perform k-means clustering
kmeans_cluster_names <- paste0("kcluster", c(2:15))
sample_290_normalized <- kmeans_clustering(
sample_290_normalized,
k_range = c(2:15),
check_stability = TRUE
)
# Plot k-means
kmeans_plot_list <- kmeans_cluster_names %>%
purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x))
cowplot::plot_grid(plotlist = kmeans_plot_list, ncol = 4)
# Perform graph-based walktrap clustering
walktrap_cluster_names <-paste0("walktrap_cluster", c(5, 10, 15, 20, 25, 50, 100))
sample_290_normalized <- graph_clustering(
sample_290_normalized,
nn_range = c(5, 10, 15, 20, 25, 50, 100),
weighting_type = "rank",
cluster_function = "walktrap",
check_stability = TRUE
)
detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# Plot
walktrap_plot_list <- walktrap_cluster_names %>%
purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x))
cowplot::plot_grid(plotlist = walktrap_plot_list, ncol = 3)
# Perform graph-based louvain clustering
louvain_cluster_names <- paste0("louvain_cluster", c(5, 10, 15, 20, 25, 50, 100))
sample_290_normalized <- graph_clustering(
sample_290_normalized,
nn_range = c(5, 10, 15, 20, 25, 50, 100),
weighting_type = "jaccard",
cluster_function = "louvain",
check_stability = TRUE
)
detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'detected tied distances to neighbors, see ?'BiocNeighbors-ties'
# Plot
louvain_plot_list <- louvain_cluster_names %>%
purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x))
cowplot::plot_grid(plotlist = louvain_plot_list, ncol = 3)
# Check the k-means cluster validity stats for each of the clusters and produce
# a summary data frame of these stats to be stored within the SCE object
sample_290_normalized <- add_metadata_clustering_stats(sample_290_normalized, kmeans_cluster_names, "kmeans")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the saved results
head(metadata(sample_290_normalized)$all_stats$kmeans)
# Preview the saved summary results
head(metadata(sample_290_normalized)$summary_stats$kmeans)
# Plot individual cluster and summary stats
kmeans_plots <- plot_clustering_validity(metadata(sample_290_normalized)$all_stats$kmeans,
metadata(sample_290_normalized)$summary_stats$kmeans,
"purity", "maximum", "cluster_names", c(2:15))
Outer names are only allowed for unnamed scalar atomic inputs
kmeans_plots
# Plot individual cluster and summary stats
kmeans_silhouette_plots <- plot_clustering_validity(metadata(sample_290_normalized)$all_stats$kmeans,
metadata(sample_290_normalized)$summary_stats$kmeans,
"width", "closest", "cluster_names", c(2:15))
Outer names are only allowed for unnamed scalar atomic inputs
kmeans_silhouette_plots
# Check the walktrap cluster validity stats for each of the clusters and produce
# a summary data frame of these stats to be stored within the SCE object
sample_290_normalized <- add_metadata_clustering_stats(sample_290_normalized, walktrap_cluster_names, "walktrap")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the saved results
head(metadata(sample_290_normalized)$all_stats$walktrap)
# Preview the saved summary results
head(metadata(sample_290_normalized)$summary_stats$walktrap)
# Plot individual cluster and summary stats
walktrap_plots <- plot_clustering_validity(metadata(sample_290_normalized)$all_stats$walktrap,
metadata(sample_290_normalized)$summary_stats$walktrap,
"purity", "maximum", "cluster_names", c(5, 10, 15, 20, 25, 50, 100))
Outer names are only allowed for unnamed scalar atomic inputs
walktrap_plots
# Plot individual cluster and summary stats
walktrap_silhouette_plots <- plot_clustering_validity(metadata(sample_290_normalized)$all_stats$walktrap,
metadata(sample_290_normalized)$summary_stats$walktrap,
"width", "closest", "cluster_names", c(5, 10, 15, 20, 25, 50, 100))
Outer names are only allowed for unnamed scalar atomic inputs
walktrap_silhouette_plots
# Check the louvain cluster validity stats for each of the clusters and produce
# a summary data frame of these stats to be stored within the SCE object
sample_290_normalized <- add_metadata_clustering_stats(sample_290_normalized, louvain_cluster_names, "louvain")
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
# Preview the saved results
head(metadata(sample_290_normalized)$all_stats$louvain)
# Preview the saved summary results
head(metadata(sample_290_normalized)$summary_stats$louvain)
# Plot individual cluster and summary stats
louvain_plots <- plot_clustering_validity(metadata(sample_290_normalized)$all_stats$louvain,
metadata(sample_290_normalized)$summary_stats$louvain,
"purity", "maximum", "cluster_names", c(5, 10, 15, 20, 25, 50, 100))
Outer names are only allowed for unnamed scalar atomic inputs
louvain_plots
# Plot individual cluster and summary stats
louvain_silhouette_plots <- plot_clustering_validity(metadata(sample_290_normalized)$all_stats$louvain,
metadata(sample_290_normalized)$summary_stats$louvain,
"width", "closest", "cluster_names", c(5, 10, 15, 20, 25, 50, 100))
Outer names are only allowed for unnamed scalar atomic inputs
louvain_silhouette_plots
# Check and plot cluster stability
kmeans_cluster_names %>%
purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))
walktrap_cluster_names %>%
purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))
louvain_cluster_names %>%
purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 ggpubr_0.4.0 bluster_1.4.0
[4] HDF5Array_1.22.1 rhdf5_2.38.0 DelayedArray_0.20.0
[7] Matrix_1.3-4 ComplexHeatmap_2.10.0 scater_1.22.0
[10] ggplot2_3.3.5 scuttle_1.4.0 SingleCellExperiment_1.16.0
[13] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1
[16] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3
[19] BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
[22] readr_2.1.1 magrittr_2.0.1
loaded via a namespace (and not attached):
[1] ggbeeswarm_0.6.0 colorspace_2.0-2 ggsignif_0.6.3 rjson_0.2.20
[5] ellipsis_0.3.2 modeltools_0.2-23 circlize_0.4.13 XVector_0.34.0
[9] GlobalOptions_0.1.2 BiocNeighbors_1.12.0 rstudioapi_0.13 clue_0.3-60
[13] farver_2.1.0 ggrepel_0.9.1 flexmix_2.3-17 fansi_0.5.0
[17] codetools_0.2-18 splines_4.1.2 sparseMatrixStats_1.6.0 doParallel_1.0.16
[21] knitr_1.36 polyclip_1.10-0 broom_0.7.10 cluster_2.1.2
[25] png_0.1-7 ggforce_0.3.3 compiler_4.1.2 backports_1.4.0
[29] assertthat_0.2.1 fastmap_1.1.0 cli_3.1.0 tweenr_1.0.2
[33] BiocSingular_1.10.0 miQC_1.2.0 htmltools_0.5.2 tools_4.1.2
[37] rsvd_1.0.5 igraph_1.2.9 gtable_0.3.0 glue_1.5.1
[41] GenomeInfoDbData_1.2.7 dplyr_1.0.7 Rcpp_1.0.7 carData_3.0-4
[45] vctrs_0.3.8 rhdf5filters_1.6.0 iterators_1.0.13 DelayedMatrixStats_1.16.0
[49] xfun_0.28 beachmat_2.10.0 lifecycle_1.0.1 irlba_2.3.3
[53] renv_0.14.0 rstatix_0.7.0 zlibbioc_1.40.0 MASS_7.3-54
[57] scales_1.1.1 hms_1.1.1 parallel_4.1.2 RColorBrewer_1.1-2
[61] yaml_2.2.1 gridExtra_2.3 foreach_1.5.1 ScaledMatrix_1.2.0
[65] BiocParallel_1.28.2 shape_1.4.6 rlang_0.4.12 pkgconfig_2.0.3
[69] bitops_1.0-7 evaluate_0.14 lattice_0.20-45 purrr_0.3.4
[73] Rhdf5lib_1.16.0 labeling_0.4.2 cowplot_1.1.1 tidyselect_1.1.1
[77] R6_2.5.1 generics_0.1.1 DBI_1.1.1 pillar_1.6.4
[81] withr_2.4.3 abind_1.4-5 RCurl_1.98-1.5 nnet_7.3-16
[85] tibble_3.1.6 crayon_1.4.2 car_3.0-12 utf8_1.2.2
[89] tzdb_0.2.0 rmarkdown_2.11 viridis_0.6.2 GetoptLong_1.0.5
[93] data.table_1.14.2 digest_0.6.29 tidyr_1.1.4 munsell_0.5.0
[97] beeswarm_0.4.0 viridisLite_0.4.0 vipor_0.4.5